ArticleMolecular biology and evolution2012
Evolution of viral proteins originated de novo by overprinting.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
89 citing papers in PubMed, 1 synthesis or guideline pooled it, 142 citations in OpenAlex.
- Pooled it
- Disruption of the nucleocapsid-RNA condensation by punicalagin is a broad-spectrum antiviral approach.Fundamental research · 2026Article
- De Novo Genes: Current Status and Future Goals.Genome biology and evolution · 2025Article
- Chasing the Ghost Proteome in the Dark Matter.Molecular & cellular proteomics : MCP · 2025Review
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Evolution of primate T-cell leukemia virus type 1 accessory genes and functional divergence of its antisense proteins.PLoS pathogens · 2025Article
- CodonTransformer: a multispecies codon optimizer using context-aware neural networks.Nature communications · 2025Article
- Yaravirus brasiliense genomic structure analysis and its possible influence on the metabolism.Genetics and molecular biology · 2025Article
- De Novo Genes.Annual review of genetics · 2024Review
- Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.Genome research · 2024Article
- How antisense transcripts can evolve to encode novel proteins.Nature communications · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss.The ISME journal · 2024Article
- Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair.Journal of molecular evolution · 2023Article
- Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty.Journal of molecular evolution · 2023Review
- Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.Microbiology spectrum · 2023Article
- Cellular and Natural Viral Engineering in Cognition-Based Evolution.Communicative & integrative biology · 2023Review
- HexSE: Simulating evolution in overlapping reading frames.Virus evolution · 2023Article
- Mechanisms of protein evolution.Protein science : a publication of the Protein Society · 2022Review
- Gene Overlapping as a Modulator ofMicroorganisms · 2022Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 4 countries.
Funding
Abstract
New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been "overprinted" by a new open reading frame, a process that generates a new protein-coding gene overlapping the ancestral gene. We analyzed the evolution of 12 experimentally validated viral genes that originated de novo and estimated their relative ages. We found that young de novo genes have a different codon usage from the rest of the genome. They evolve rapidly and are under positive or weak purifying selection. Thus, young de novo genes might have strain-specific functions, or no function, and would be difficult to detect using current genome annotation methods that rely on the sequence signature of purifying selection. In contrast to young de novo genes, older de novo genes have a codon usage that is similar to the rest of the genome. They evolve slowly and are under stronger purifying selection. Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.